peptide/mass are counted per valid proteins

src/core/identificationgroup.cpp

@@ -42,7 +42,7 @@ IdentificationGroup::~IdentificationGroup()
 }
 
 const PtmGroupingExperiment * IdentificationGroup::getPtmGroupingExperiment() const {
-  return _p_grp_ptm_experiment;
+    return _p_grp_ptm_experiment;
 }
 const GroupStore & IdentificationGroup::getGroupStore() const {
     return _group_store;
@@ -52,7 +52,9 @@ unsigned int IdentificationGroup::countPeptideMass(ValidationState state) const
 
     std::vector<pappso::GrpPeptide *> count_peptide_mass;
     for (auto & p_protein_match : _protein_match_list) {
-        p_protein_match->countPeptideMass(count_peptide_mass, state);
+        if (p_protein_match->getValidationState() >= state) {
+            p_protein_match->countPeptideMass(count_peptide_mass, state);
+        }
     }
     std::sort(count_peptide_mass.begin(), count_peptide_mass.end());
     auto last = std::unique(count_peptide_mass.begin(),count_peptide_mass.end());
@@ -63,7 +65,9 @@ unsigned int IdentificationGroup::countPeptideMassSample(ValidationState state)
 
     std::vector<std::size_t> count_peptide_mass_sample;
     for (auto & p_protein_match : _protein_match_list) {
-        p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+        if (p_protein_match->getValidationState() >= state) {
+            p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+        }
     }
     std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
     auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
@@ -74,7 +78,9 @@ unsigned int IdentificationGroup::countDecoyPeptideMassSample(ValidationState st
     std::vector<std::size_t> count_peptide_mass_sample;
     for (auto & p_protein_match : _protein_match_list) {
         if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
-            p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+            if (p_protein_match->getValidationState() >= state) {
+                p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+            }
         }
     }
     std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
@@ -86,11 +92,11 @@ unsigned int IdentificationGroup::countDecoyPeptideMassSample(ValidationState st
 unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
     unsigned int i=0;
     for (auto & p_protein_match : _protein_match_list) {
-        //if (p_protein_match->getValidationState() == state) {
-        if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
-            i+=p_protein_match->countPeptideMatch(state);
+        if (p_protein_match->getValidationState() >= state) {
+            if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
+                i+=p_protein_match->countPeptideMatch(state);
+            }
         }
-        //}
     }
     return i;
 }
@@ -108,9 +114,9 @@ unsigned int IdentificationGroup::countDecoyProteinMatch(ValidationState state)
 unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
     unsigned int i=0;
     for (auto & p_protein_match : _protein_match_list) {
-        //if (p_protein_match->getValidationState() >= state) {
-        i+=p_protein_match->countPeptideMatch(state);
-        //}
+        if (p_protein_match->getValidationState() >= state) {
+            i+=p_protein_match->countPeptideMatch(state);
+        }
     }
     return i;
 }
@@ -203,6 +209,7 @@ std::size_t IdentificationGroup::countSubGroup()const {
 }
 
 void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
+    std::set<PeptideEvidence *> already_counted;
     for (auto & p_protein_match : _protein_match_list) {
         if (p_protein_match->getValidationState() >= state) {
             if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) {